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Hi--
>
> I go back to check my pdb file and then find possible mistakes.
> The initial structure uses two long linkers to connect three chains.
> When I prepare my pdb file, I delete these linkers without giving the
> different chain number. This may be the point.
>
sounds like you're making progress...
> Here, I have another question. If there is a jump on residue number due
> to the chain break, can addAtom.py read through sequence file to match
> the corresponding atoms in pdb file?
>
For this, modify the addAtoms.py script as follows:
1) split the seq string into two, named say seq1 and seq2, broken at the
chain break.
2) call psfGen.seqToPSF twice: first using seq1 and startResid=1
second using seq2 and the appropriate startResid
hope this helps--
Charles
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